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Structure of a GH39 Beta-xylosidase from Caulobacter crescentus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EKJ PDB entry 4EKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1 M MES, 12% PEG6000, 0.05 M NaCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.287 α = 90 b = 57.347 β = 91.38 c = 94.05 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2012-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.60 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 17.4 96.2 25413 25082 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 96.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4EKJ 2.1 17.4 25082 24125 1288 96.04 0.231 0.228 0.2348 0.286 0.2878 RANDOM 16.78
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.59 -0.15 -2.05 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.239 r_dihedral_angle_4_deg 20.538 r_dihedral_angle_3_deg 17.281 r_dihedral_angle_1_deg 7.169 r_angle_refined_deg 1.9 r_angle_other_deg 1.007 r_chiral_restr 0.122 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.239 r_dihedral_angle_4_deg 20.538 r_dihedral_angle_3_deg 17.281 r_dihedral_angle_1_deg 7.169 r_angle_refined_deg 1.9 r_angle_other_deg 1.007 r_chiral_restr 0.122 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3558 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 12
Software Software Software Name Purpose NatXray data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling